Gerstel Markus, Deane Charlotte M, Garman Elspeth F
Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.
J Synchrotron Radiat. 2015 Mar;22(2):201-12. doi: 10.1107/S1600577515002131. Epub 2015 Feb 14.
Radiation damage impedes macromolecular diffraction experiments. Alongside the well known effects of global radiation damage, site-specific radiation damage affects data quality and the veracity of biological conclusions on protein mechanism and function. Site-specific radiation damage follows a relatively predetermined pattern, in that different structural motifs are affected at different dose regimes: in metal-free proteins, disulfide bonds tend to break first followed by the decarboxylation of aspartic and glutamic acids. Even within these damage motifs the decay does not progress uniformly at equal rates. Within the same protein, radiation-induced electron density decay of a particular chemical group is faster than for the same group elsewhere in the protein: an effect known as preferential specific damage. Here, BDamage, a new atomic metric, is defined and validated to recognize protein regions susceptible to specific damage and to quantify the damage at these sites. By applying BDamage to a large set of known protein structures in a statistical survey, correlations between the rates of damage and various physicochemical parameters were identified. Results indicate that specific radiation damage is independent of secondary protein structure. Different disulfide bond groups (spiral, hook, and staple) show dissimilar radiation damage susceptibility. There is a consistent positive correlation between specific damage and solvent accessibility.
辐射损伤会妨碍大分子衍射实验。除了众所周知的整体辐射损伤效应外，位点特异性辐射损伤会影响数据质量以及关于蛋白质机制和功能的生物学结论的准确性。位点特异性辐射损伤遵循相对预先确定的模式，即不同的结构基序在不同的剂量范围内受到影响：在无金属蛋白质中，二硫键往往首先断裂，随后是天冬氨酸和谷氨酸的脱羧。即使在这些损伤基序内，衰变也不会以相同的速率均匀进行。在同一蛋白质中，特定化学基团的辐射诱导电子密度衰减比蛋白质其他部位的同一基团更快：这种效应称为优先特异性损伤。在此，定义并验证了一种新的原子指标BDamage，以识别易受特异性损伤的蛋白质区域并量化这些位点的损伤。通过在统计调查中将BDamage应用于大量已知蛋白质结构，确定了损伤速率与各种物理化学参数之间的相关性。结果表明，特异性辐射损伤与蛋白质二级结构无关。不同的二硫键基团（螺旋、钩状和订书钉状）表现出不同的辐射损伤敏感性。特异性损伤与溶剂可及性之间存在一致的正相关。
